Global concern surrounds the contamination of dairy products with aflatoxin M1 (AFM1), a mycotoxin found in the milk of ruminants fed with aflatoxin B1-contaminated feed. Among dairy products, cheese is of the foods with the highest concentration of AFM1 mycotoxin, although the reported levels vary widely. This study analyzed AFM1 levels in 100 commercial cheeses produced and marketed in Spain. AFM1 was detected in 51% of the samples, with concentrations ranging from 8.1 to 470.7 ng/kg. The milk type and animal species significantly influenced the contamination levels with a higher prevalence and mean contamination rates in cheeses made from cow’s milk (67.6% and 43 ng/kg) and pasteurized milk (60.7% and 33 ng/kg). The degree of ripening of the cheese did not significantly influence the contamination of the products, although the occurrence and average levels observed in fresh cheeses (63.0% and 53 ng/kg) were higher than those observed in mature (48.0% and 13 ng/kg) and semi-mature cheeses (43.5% and 11 ng/kg). There were no significant differences in the contamination levels between artisanal (56.6% and 33 ng/kg) and industrial (44.7% and 12 ng/kg) cheeses. The dietary exposure estimates for average consumers were low across all age groups: 0.004 ng/kg bw/day (adults), 0.007 ng/kg bw/day (adolescents), 0.025 ng/kg bw/day (children), and 0.081 ng/kg bw/day (toddlers). Consequently, the Margin of Exposure (MOE) values exceeded 10,000, indicating a low public health concern, except for toddlers in the 95th percentile of consumption.